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DISCOVERY STUDIO

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November 2008

Accelrys Discovery Studio Newsletter

News and Information
DS Tips and Tricks
Featured Journal Articles
DS Community Forum Highlight
Script or Protocol of the Month

News and Information

Tips & Tricks

It is possible to create angle monitors between atoms that are not bound. However, since the selection order is not considered there are three possible angles for any selection of three atoms. Discovery Studio lets you specify the desired angle by first selecting the angle monitor then open "Angle Monitor Attributes" by selecting the angle monitor and right clicking on the selected monitor you can set the "Orientation" parameter to either "First Angle", "Second Angle" or "Third Angle".

Featured Journal Article

The Hypogen functionality in Catalyst (now available in Discovery Studio as the "3D QSAR Pharmacophore Generation" protocol) was used to generate a chemical function-based pharmacophore model from a training set of 26 kappa opioid receptor agonists exhibiting Ki values ranging between 0.015 nM and 2300 nM. The authors write that "to our knowledge this is the first attempt to account for several structurally unrelated KOP agonists belonging to different activity classes."

Nidhi Singh a, Tammy L. Nolan a, Christopher R. McCurdy, J. Mol. Graph Model. 2008 Sep;27(2):131-139. Chemical function-based pharmacophore development for novel, selective kappa opioid receptor agonists.

Community Forum Highlight

A commonly requested enhancement of Discovery Studio's "Looper" protocol has been posted to the forums which returns the loops fully built-in to the full 3D protein. You can access the posting here.

Script of the Month

It is some times useful to visualize specifically what regions of a structure are the main contributors to the (high) energy of a structure. One way to do this is to record then visuallize the forces present on each atom. These forces come from the effect of the force field terms on each atom. Using CHARMm it is possible to store the forces on each atom by doing a slightly modified energy calculation. The ColorForce protocol performs this modified energy calculation then stores the force on each atom as the Isotropic Displacement property in the msv file such that low force atoms are BLUE fading to white as the "target" force threshhold is reached, then ranging from white to RED at twice the threshhold force. This protocol requires a CHARMm (Simulations) license to run. In the image below a transparent surface colored based on atom coloring has been added. The protocol is available here.

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